Search results for "phylogenetic"
showing 10 items of 1179 documents
Comparative Genomics of Blattabacterium cuenoti: The Frozen Legacy of an Ancient Endosymbiont Genome
2013
Many insect species have established long-term symbiotic relationships with intracellular bacteria. Symbiosis with bacteria has provided insects with novel ecological capabilities, which have allowed them colonize previously unexplored niches. Despite its importance to the understanding of the emergence of biological complexity, the evolution of symbiotic relationships remains hitherto a mystery in evolutionary biology. In this study, we contribute to the investigation of the evolutionary leaps enabled by mutualistic symbioses by sequencing the genome of Blattabacterium cuenoti, primary endosymbiont of the omnivorous cockroach Blatta orientalis, and one of the most ancient symbiotic associa…
Emergence and Phylodynamics of Citrus tristeza virus in Sicily, Italy
2013
Citrus tristeza virus (CTV) outbreaks were detected in Sicily island, Italy for the first time in 2002. To gain insight into the evolutionary forces driving the emergence and phylogeography of these CTV populations, we determined and analyzed the nucleotide sequences of the p20 gene from 108 CTV isolates collected from 2002 to 2009. Bayesian phylogenetic analysis revealed that mild and severe CTV isolates belonging to five different clades (lineages) were introduced in Sicily in 2002. Phylogeographic analysis showed that four lineages co-circulated in the main citrus growing area located in Eastern Sicily. However, only one lineage (composed of mild isolates) spread to distant areas of Sici…
Population genetics of cucumber mosaic virus infecting medicinal, aromatic and ornamental plants from northern Italy
2012
An epidemiological survey carried at the Herb Garden of Casola Valsenio (Emilia Romagna region; Northern Italy) from 2006 to 2009 resulted in finding Cucumber mosaic virus (CMV) as the infectious agent of several ornamental, medicinal and aromatic plants. All CMV-infected plant species showed leaf symptoms followed, in some cases, by flower colour-breaking and stunting. Genetic analysis consisted in the characterization of movement protein gene of each CMV-isolate by single strand polymorphism analysis and sequencing. Phylogenetic trees identified only two isolates as member of subgroup II, while all other isolates were part of subgroup IA. This survey confirms an unexpected increment of CM…
Genetic variability and evolutionary analysis of parietaria mottle virus: role of selection and genetic exchange
2015
[EN] The genetic variability and evolution of parietaria mottle virus (PMoV) of the genus Ilarvirus was studied by analyzing nucleotide sequences of 2b and CP genes from isolates collected in different countries. Phylogenetic analysis showed that PMoV isolates clustered in different clades: one (clade I) composed of only Italian isolates and three clades (clades II-IV) including the Spanish isolates. The Greek isolate GrT-1 used in this study was in clade IV for the CP phylogenetic tree whereas it formed a separate branch in the 2b phylogenetic tree. The nucleotide sequence diversity of both the 2b and CP genes was low (0.062 +/- A 0.006 and 0.063 +/- A 0.006 for 2b and CP, respectively) bu…
Comparative Sequence Analysis ofMycobacterium lepraeand the New Leprosy-CausingMycobacterium lepromatosis
2009
ABSTRACTMycobacterium lepromatosisis a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence fromMycobacterium leprae, a well-known cause of leprosy, that justifies the status ofM. lepromatosisas a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences withM. lepraesequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes…
Taxas de substituições das Annonaceas: uma perspectiva do modelo códon
2014
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these…
The migratory birds: novel ecological niche of fungal diversity?
2015
Francesca et al (2010) studied the ecology of wine yeasts associated to birds caught in vineyards. The same authors were able to prove that migratory birds might carry living pro-technological yeasts for about 12 hours from the ingestion of inoculated feed (Francesca et al 2012). In subsequent studies, they tried to demonstrate that microorganisms are not only transported for a short period by birds, but microorganisms might be adapted to the specific conditions (body temperature about 42 °C and low pH) of the intestinal tract of birds. Hence, it was demonstrated that the majority of isolates carried by birds are thermotolerant. The most interesting results were the isolation of two new spe…
Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants.
2006
The internal transcribed spacers (ITS) of the nuclear ribosomal 18S–5.8S–26S cistron continue to be the most popular non-plastid region for species-level phylogenetic studies of plant groups despite the early warnings about their potential Xaws, which may ultimately result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (lowcopy nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for nonmodel organisms requires an investment in time and eVort that hinders its use as a real practical alternative for many labs. It is here argued that ITS sequences, desp…
Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea
2009
5 pages, 2 figures, 1 table
Acyl Transferase Domains of Putative Polyketide Synthase (PKS) Genes in Aspergillus and Penicillium Producers of Ochratoxin A and the Evaluation of P…
2009
Fungal polyketide synthases (PKS) are responsible for the biosynthesis of several mycotoxins and other secondary metabolites. PKS genes in ochratoxin producing species from Aspergillus and Penicillum genera have been identified using a degenerate primer pair developed for the acyl transferase (AT) domain of fungal PKSs. Sequences of AT domains were aligned and analyzed using phylogenetic methods. The AT domain sequences appeared to be specific for a particular type of fungal PKSs and were related to PKSs involved in different mycotoxin biosynthesis pathways, including ochratoxin A. We have also developed primers suitable for amplifying AT domain sequences in strains belonging to the A. nig…